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- PDB-4qay: Crystal structure of TamA POTRA domains -

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Basic information

Entry
Database: PDB / ID: 4qay
TitleCrystal structure of TamA POTRA domains
ComponentsTranslocation and assembly module TamA
KeywordsTRANSPORT PROTEIN / POLYPEPTIDE TRANSPORT-ASSOCIATED / AUTOTRANSPORTER BIOGENESIS / OUTER MEMBRANE PROTEIN
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
TamA, POTRA domain 1 / POTRA domain TamA domain 1 / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain ...TamA, POTRA domain 1 / POTRA domain TamA domain 1 / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Autotransporter assembly factor TamA
Similarity search - Component
Biological specieshuman gut metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsWojdyla, J.A. / Mosbahi, K. / Walker, D. / Kleanthous, C.
CitationJournal: To be Published
Title: Recognition of autotransporter passenger domains by the TAM complex
Authors: Josts, I. / Mosbahi, K. / Wojdyla, J.A. / Kelly, S. / Kleanthous, C. / Byron, O. / Smith, B.O. / Walker, D.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translocation and assembly module TamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9313
Polymers31,7411
Non-polymers1902
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Translocation and assembly module TamA
hetero molecules

A: Translocation and assembly module TamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8626
Polymers63,4822
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-1,-x-1,-z-1/21
Buried area3140 Å2
ΔGint-42 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.455, 78.455, 152.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

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Components

#1: Protein Translocation and assembly module TamA


Mass: 31740.877 Da / Num. of mol.: 1 / Fragment: TamA POTRA domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gut metagenome (others) / Gene: Q604_UNBC18528G0002, TamA / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W1WMC8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.9795
SYNCHROTRONDiamond I0320.9795
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 4, 2012
DECTRIS PILATUS 6M-F2PIXELMay 12, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. all: 20576 / Num. obs: 20535 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXSphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.556 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26082 1048 5.1 %RANDOM
Rwork0.19774 ---
obs0.20099 19429 99.79 %-
all-19470 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 10 142 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192030
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.982750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4855253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65322.95998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1711522
X-RAY DIFFRACTIONr_chiral_restr0.1310.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211547
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 64 -
Rwork0.3 1219 -
obs--97.34 %

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